With advancements in molecular biology, many genes associated with lipid/lipoprotein disorders and, in particular, with atherosclerotic cardiovascular disease have been recently identified and characterized. We have been studying the gene for apolipoprotein(a) (apo(a)) and its product for improved diagnosis of patients and for a better understanding of the pathogenic events involved in the development of atherosclerotic cardiovascular disease. Recently, we optimized two major pulsed-field gel electrophoretic (PFGE) techniques, the clamped homogeneous electrical field (CHEF) and field inversion gel electrophoresis (FIGE), for separating medium- size DNA molecules such as the apo(a) genes. This step allowed us to develop a reproducible nomenclature based on the so-called kringle number (the number of kringle intravenous repeats) for apo(a) isoforms in the serum and discontinue the use of earlier arbitrary nomenclatures. We have also made technical improvements in apo(a) phenotyping with applicability to the separation and immunoblotting of proteins in general. We showed that large protein molecules such as the isoforms of apo(a) can be conveniently and efficiently separated by the CHEF and FIGE methods that were originally developed to separate large DNA molecules. Also, we developed a rapid, highly efficient, and inexpensive immunoblotting method for apo(a) that is based on downward capillary action. With these technical improvements in both the detection and classification of various apo(a) isoforms, we are now studying the possible relationship between these isoforms and the serum lipoprotein(a) (Lp(a)) concentration. In collaborative clinical studies, we discovered specific associations between apo(a) isoforms and the occurrence of thromboembolic events in patients with systemic lupus erythematosus. Additional studies are under way to explore associations between various apo(a) isoforms and fibrinolysis in patients undergoing extreme variations in thyroid status (from hyperthyroid through euthyroid, severely hypothyroid, and euthyroid to overtly hyperthyroid again) and possible associations among apo(a) isoforms, serum Lp(a) concentration, and gonadal steroids (particularly estrogen) in healthy subjects.